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library(png)
library(readxl)
library(knitr)
library(cowplot)
library(ggplot2)
library(magick)
library(png)
library(readxl)
library(knitr)
library(cowplot)
library(ggplot2)
library(magick)

filename_sample_Combine_pairs <- paste0('C:/Users/Sylvia/Dropbox (Partners HealthCare)/Sylvia_Romanos/scRNASeq/Data/sample_Combine_pairs.xlsx')
sample_Combine_pairs <- read_excel(filename_sample_Combine_pairs)


sample_type = 'PrePostNBM'
integrate_merge = 'Merge'
folder_base_output = paste0('C:/Users/Sylvia/Dropbox (Partners HealthCare)/Sylvia_Romanos/scRNASeq/Code/Output/',integrate_merge ,' All/',sample_type,'/')
  
for (i in 1:22){
  print(i)
  if (sample_Combine_pairs$'Dexa or not'[i] != 'NBM'){
    
    sample_pre = sample_Combine_pairs$'Sample Pre BM'[i]
    sample_post = sample_Combine_pairs$'Sample Post BM'[i]
    
    print(paste0('Dexa ',sample_Combine_pairs$'Dexa or not'[i]))
    print(paste0('Sample Pre:',sample_pre ))
    print(paste0('Sample Pre:',sample_post ))
    
    folder_input_pre = paste0(folder_base_output,'Samples Seperate/',sample_pre,'/Cluster/PCA20/res1/')
    folder_input_post = paste0(folder_base_output,'Samples Seperate/',sample_post,'/Cluster/PCA20/res1/')
    
    filename_umap_pre = paste0(folder_input_pre,'ClusterUmap_PCA20_res1_label.png')
    filename_heatmap_pre = paste0(folder_input_pre,'HeatMap_PCA20_res1_label.png')
    
    filename_umap_post = paste0(folder_input_post,'ClusterUmap_PCA20_res1_label.png')
    filename_heatmap_post = paste0(folder_input_post,'HeatMap_PCA20_res1_label.png')
    
    label_list = c(paste0(sample_pre, ' Pre Dexa ',sample_Combine_pairs$'Dexa or not'[i] ),
                   paste0(sample_post, ' Post Dexa ',sample_Combine_pairs$'Dexa or not'[i] ))
    p1 <- ggdraw() + draw_image(filename_umap_pre, scale = 1) 
    p2 <- ggdraw() + draw_image(filename_umap_post, scale = 1) 
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)
    
    p1 <- ggdraw() + draw_image(filename_heatmap_pre, scale = 1)
    p2 <- ggdraw() + draw_image(filename_heatmap_post, scale = 1)
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)


  }else{
    
    sample = sample_Combine_pairs$'Sample Pre BM'[i]

    print(paste0('Dexa ',sample_Combine_pairs$'Dexa or not'[i]))
    print(paste0('Sample: ',sample ))

    folder_input_pre = paste0(folder_base_output,'Samples Seperate/',sample,'/Cluster/PCA20/res1/')

    filename_umap_pre = paste0(folder_input_pre,'ClusterUmap_PCA20_res1_label.png')
    filename_heatmap_pre = paste0(folder_input_pre,'HeatMap_PCA20_res1_label.png')

    label_list = c(paste0(sample, ' ', sample_Combine_pairs$'Dexa or not'[i] ))
    p1 <- ggdraw() + draw_image(filename_umap_pre, scale = 1) 
    p2 <- ggdraw() + draw_image(filename_heatmap_pre, scale = 1) 
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)
  

  }
      
}

[1] 1
[1] "Dexa No"
[1] "Sample Pre:GL1024BM"
[1] "Sample Pre:GL1290BM"
[1] 2
[1] "Dexa No"
[1] "Sample Pre:GL1110BM"
[1] "Sample Pre:GL1420BM"
[1] 3
[1] "Dexa No"
[1] "Sample Pre:GL1160BM"
[1] "Sample Pre:GL1497BM"
[1] 4
[1] "Dexa Yes"
[1] "Sample Pre:GL1080BM"
[1] "Sample Pre:GL1374BM"
[1] 5
[1] "Dexa Yes"
[1] "Sample Pre:GL1305BM"
[1] "Sample Pre:GL1786BM"
[1] 6
[1] "Dexa Yes"
[1] "Sample Pre:GL1587BM"
[1] "Sample Pre:GL2264BM"
[1] 7
[1] "Dexa Yes"
[1] "Sample Pre:GL1445BM"
[1] "Sample Pre:GL2156BM"
[1] 8
[1] "Dexa Yes"
[1] "Sample Pre:GL1371BM"
[1] "Sample Pre:GL2090BM"
[1] 9
[1] "Dexa Yes"
[1] "Sample Pre:GL1478BM"
[1] "Sample Pre:GL2320BM"
[1] 10
[1] "Dexa Yes"
[1] "Sample Pre:GL2257BM"
[1] "Sample Pre:GL2941BM"
[1] 11
[1] "Dexa Yes"
[1] "Sample Pre:GL1036BM"
[1] "Sample Pre:GL1320BM"
[1] 12
[1] "Dexa Yes"
[1] "Sample Pre:GL1797BM"
[1] "Sample Pre:GL2697BM"
[1] 13
[1] "Dexa NBM"
[1] "Sample: NBM1CD45P"
[1] 14
[1] "Dexa NBM"
[1] "Sample: NBM2CD45P"
[1] 15
[1] "Dexa NBM"
[1] "Sample: NBM3CD45P"
[1] 16
[1] "Dexa NBM"
[1] "Sample: NBM4CD138N"
[1] 17
[1] "Dexa NBM"
[1] "Sample: NBM6CD138N"
[1] 18
[1] "Dexa NBM"
[1] "Sample: NBM7CD138N"
[1] 19
[1] "Dexa NBM"
[1] "Sample: NBM9CD138N"
[1] 20
[1] "Dexa NBM"
[1] "Sample: NBM10CD138N"
[1] 21
[1] "Dexa NBM"
[1] "Sample: NBM11CD138N"
[1] 22
[1] "Dexa NBM"
[1] "Sample: NBM12CD138N"

NA

filename_sample_Combine_pairs <- paste0('C:/Users/Sylvia/Dropbox (Partners HealthCare)/Sylvia_Romanos/scRNASeq/Data/sample_Combine_pairs.xlsx')
sample_Combine_pairs <- read_excel(filename_sample_Combine_pairs)


sample_type = 'PrePost'
integrate_merge = 'Integrate'
folder_base_output = paste0('C:/Users/Sylvia/Dropbox (Partners HealthCare)/Sylvia_Romanos/scRNASeq/Code/Output/',integrate_merge ,' All/',sample_type,'/')
  
for (i in 1:12){
  print(i)
  if (sample_Combine_pairs$'Dexa or not'[i] != 'NBM'){
    
    PCA = 15
    res = 1
    sample_pre = sample_Combine_pairs$'Sample Pre BM'[i]
    sample_post = sample_Combine_pairs$'Sample Post BM'[i]
    
    print(paste0('Dexa ',sample_Combine_pairs$'Dexa or not'[i]))
    print(paste0('Sample Pre:',sample_pre ))
    print(paste0('Sample Pre:',sample_post ))
    
    folder_input_pre = paste0(folder_base_output,'Samples Seperate/',sample_pre,'/Cluster/PCA',PCA,'/res',res,'/')
    folder_input_post = paste0(folder_base_output,'Samples Seperate/',sample_post,'/Cluster/PCA',PCA,'/res',res,'/')
    
    filename_umap_pre = paste0(folder_input_pre,'ClusterUmap_PCA',PCA,'_res',res,'_label.png')
    filename_heatmap_pre = paste0(folder_input_pre,'HeatMap_PCA',PCA,'_res',res,'_label.png')
    
    filename_umap_post = paste0(folder_input_post,'ClusterUmap_PCA',PCA,'_res',res,'_label.png')
    filename_heatmap_post = paste0(folder_input_post,'HeatMap_PCA',PCA,'_res',res,'_label.png')
    
    label_list = c(paste0(sample_pre, ' Pre Dexa ',sample_Combine_pairs$'Dexa or not'[i] ),
                   paste0(sample_post, ' Post Dexa ',sample_Combine_pairs$'Dexa or not'[i] ))
    p1 <- ggdraw() + draw_image(filename_umap_pre, scale = 1) 
    p2 <- ggdraw() + draw_image(filename_umap_post, scale = 1) 
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)
    
    p1 <- ggdraw() + draw_image(filename_heatmap_pre, scale = 1)
    p2 <- ggdraw() + draw_image(filename_heatmap_post, scale = 1)
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)


  }else{
    
    sample = sample_Combine_pairs$'Sample Pre BM'[i]

    print(paste0('Dexa ',sample_Combine_pairs$'Dexa or not'[i]))
    print(paste0('Sample: ',sample ))

    folder_input_pre = paste0(folder_base_output,'Samples Seperate/',sample,'/Cluster/PCA20/res1/')

    filename_umap_pre = paste0(folder_input_pre,'ClusterUmap_PCA20_res1_label.png')
    filename_heatmap_pre = paste0(folder_input_pre,'HeatMap_PCA20_res1_label.png')

    label_list = c(paste0(sample, ' ', sample_Combine_pairs$'Dexa or not'[i] ))
    p1 <- ggdraw() + draw_image(filename_umap_pre, scale = 1) 
    p2 <- ggdraw() + draw_image(filename_heatmap_pre, scale = 1) 
    plot = plot_grid(p1, p2,labels=label_list)
    print(plot)
  

  }
      
}

[1] 1
[1] "Dexa No"
[1] "Sample Pre:GL1024BM"
[1] "Sample Pre:GL1290BM"
[1] 2
[1] "Dexa No"
[1] "Sample Pre:GL1110BM"
[1] "Sample Pre:GL1420BM"
[1] 3
[1] "Dexa No"
[1] "Sample Pre:GL1160BM"
[1] "Sample Pre:GL1497BM"
[1] 4
[1] "Dexa Yes"
[1] "Sample Pre:GL1080BM"
[1] "Sample Pre:GL1374BM"
[1] 5
[1] "Dexa Yes"
[1] "Sample Pre:GL1305BM"
[1] "Sample Pre:GL1786BM"
[1] 6
[1] "Dexa Yes"
[1] "Sample Pre:GL1587BM"
[1] "Sample Pre:GL2264BM"
[1] 7
[1] "Dexa Yes"
[1] "Sample Pre:GL1445BM"
[1] "Sample Pre:GL2156BM"
[1] 8
[1] "Dexa Yes"
[1] "Sample Pre:GL1371BM"
[1] "Sample Pre:GL2090BM"
[1] 9
[1] "Dexa Yes"
[1] "Sample Pre:GL1478BM"
[1] "Sample Pre:GL2320BM"
[1] 10
[1] "Dexa Yes"
[1] "Sample Pre:GL2257BM"
[1] "Sample Pre:GL2941BM"
[1] 11
[1] "Dexa Yes"
[1] "Sample Pre:GL1036BM"
[1] "Sample Pre:GL1320BM"
[1] 12
[1] "Dexa Yes"
[1] "Sample Pre:GL1797BM"
[1] "Sample Pre:GL2697BM"